ZGPAT zinc finger CCCH-type and G-patch domain containing [Homo sapiens (human)] - Gene

Summary

Official Symbol: ZGPATprovided by HGNC
Official Full Name: zinc finger CCCH-type and G-patch domain containingprovided by HGNC
Primary source: HGNC:HGNC:15948
See related: Ensembl:ENSG00000197114 MIM:619577; AllianceGenome:HGNC:15948
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: ZIP; ZC3H9; GPATC6; GPATCH6; ZC3HDC9; KIAA1847
Summary: Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of epidermal growth factor-activated receptor activity and negative regulation of transcription by RNA polymerase II. Located in nucleoplasm and plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in liver (RPKM 22.1), kidney (RPKM 17.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 20q13.33

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (63707442..63736142)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (65527749..65556418)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (62338794..62367494)

Chromosome 20 - NC_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Data suggest that ZIP, USP39, Prp24/p100/SART3, and Prp43 associate to form complex instrumental in spliceosome assembly; ZIP regulates pre-mRNA splicing of USP39 independent of RNA binding; stable 35S tri-snRNP particles are enriched in Cajal body. (USP39 = ubiquitin specific peptidase 39; SART3 = squamous cell carcinoma antigen recognised by T cells 3; Prp43 = RNA helicase Prp43)
Title: Identification of a 35S U4/U6.U5 tri-small nuclear ribonucleoprotein (tri-snRNP) complex intermediate in spliceosome assembly.
sZIP, an alternative splice variant of ZIP, antagonizes transcription repression and growth inhibition by ZIP in liver neoplasms.
Title: sZIP, an alternative splice variant of ZIP, antagonizes transcription repression and growth inhibition by ZIP.
Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: Genome-wide searching of rare genetic variants in WTCCC data.
Observational study of gene-disease association. (HuGE Navigator)
Title: Investigation of reported associations between the 20q13 and 21q22 loci and pediatric-onset Crohn's disease in Canadian children.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array. EBI GWAS Catalog EBI GWAS CatalogPubMed
Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of zinc finger, CCCH-type with G patch domain (ZGPAT) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Vpr	vpr	HIV-1 Vpr induces the degradation of ZIP/sZIP through the DCAF1 ubiquitin ligase, while VprQ65R mutant impairs the Vpr-induced degradation of ZIP/sZIP	PubMed
	vpr	HIV-1 Vpr forms a complex by recruiting RbAp46, HAT1, ZIP/sZIP, and Cul4A	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH101996 (e-PCR)
- UniSTS:96330

RH75350 (e-PCR)
- UniSTS:83812

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of epidermal growth factor-activated receptor activity	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	ISA Inferred from Sequence Alignment more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: zinc finger CCCH-type with G patch domain-containing protein

Names: g patch domain-containing protein 6; zinc finger CCCH domain-containing protein 9; zinc finger and G patch domain-containing protein; zinc finger, CCCH-type with G patch domain

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001083113.2 → NP_001076582.1 zinc finger CCCH-type with G patch domain-containing protein isoform c

See identical proteins and their annotated locations for NP_001076582.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and uses an alternate in-frame splice site in the middle portion of the coding region, compared to variant 1. This results in a shorter protein (isoform c), compared to isoform a. Variants 3, 4 and 5 encode the same isoform (c).

Source sequence(s)

AB058750, BC019338, DA252406

Consensus CDS

CCDS13535.1

UniProtKB/TrEMBL

A0A0S2Z5X3, A0A0S2Z6H0

Related

ENSP00000391176.1, ENST00000448100.6

Conserved Domains (3) summary

cd04508
Location:221 → 251

TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...

smart00356
Location:178 → 199

ZnF_C3H1; zinc finger

pfam01585
Location:313 → 354

G-patch; G-patch domain
NM_001195653.2 → NP_001182582.1 zinc finger CCCH-type with G patch domain-containing protein isoform c

See identical proteins and their annotated locations for NP_001182582.1

Status: VALIDATED

Description

Transcript Variant: This variant (5) differs in the 5' UTR and uses an alternate in-frame splice site in the middle portion of the coding region, compared to variant 1. This results in a shorter protein (isoform c), compared to isoform a. Variants 3, 4 and 5 encode the same isoform (c).

Source sequence(s)

AK314726, BC019338, BC032612

Consensus CDS

CCDS13535.1

UniProtKB/TrEMBL

A0A0S2Z5X3, A0A0S2Z6H0

Related

ENSP00000358984.3, ENST00000369967.7

Conserved Domains (3) summary

cd04508
Location:221 → 251

TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...

smart00356
Location:178 → 199

ZnF_C3H1; zinc finger

pfam01585
Location:313 → 354

G-patch; G-patch domain
NM_001195654.2 → NP_001182583.1 zinc finger CCCH-type with G patch domain-containing protein isoform d

Status: VALIDATED

Description

Transcript Variant: This variant (6) uses two alternate in-frame splice sites in the middle portion of the coding region, compared to variant 1. This results in a shorter protein (isoform d), compared to isoform a.

Source sequence(s)

BC019338, BC032612, DA055150

Consensus CDS

CCDS56203.1

UniProtKB/TrEMBL

A0A0S2Z6H0

Related

ENSP00000349634.4, ENST00000357119.8

Conserved Domains (3) summary

cd04508
Location:221 → 251

TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...

smart00356
Location:178 → 199

ZnF_C3H1; zinc finger

pfam01585
Location:304 → 345

G-patch; G-patch domain
NM_032527.5 → NP_115916.3 zinc finger CCCH-type with G patch domain-containing protein isoform a

See identical proteins and their annotated locations for NP_115916.3

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).

Source sequence(s)

AK027878, BC019338, BC032612, DA055150

Consensus CDS

CCDS13534.1

UniProtKB/Swiss-Prot

E1P5K1, Q4VXN9, Q5JWI9, Q5JWJ0, Q8N5A5, Q8NC55, Q8WUV4, Q96JI0, Q96JU4, Q9H401

UniProtKB/TrEMBL

A0A0S2Z6H0

Related

ENSP00000332013.5, ENST00000328969.5

Conserved Domains (3) summary

cd04508
Location:221 → 251

TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...

smart00356
Location:178 → 199

ZnF_C3H1; zinc finger

pfam01585
Location:333 → 374

G-patch; G-patch domain
NM_181485.3 → NP_852150.2 zinc finger CCCH-type with G patch domain-containing protein isoform c

See identical proteins and their annotated locations for NP_852150.2

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate in-frame splice site in the middle portion of the coding region, compared to variant 1. This results in a shorter protein (isoform c), compared to isoform a. Variants 3, 4 and 5 encode the same isoform (c).

Source sequence(s)

AL121845, BC019338, BC032612, DA848516

Consensus CDS

CCDS13535.1

UniProtKB/TrEMBL

A0A0S2Z5X3, A0A0S2Z6H0

Related

ENSP00000348242.6, ENST00000355969.11

Conserved Domains (3) summary

cd04508
Location:221 → 251

TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...

smart00356
Location:178 → 199

ZnF_C3H1; zinc finger

pfam01585
Location:313 → 354

G-patch; G-patch domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000020.11 Reference GRCh38.p14 Primary Assembly

Range

63707442..63736142

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060944.1 Alternate T2T-CHM13v2.0

Range

65527749..65556418

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_181484.1: Suppressed sequence

Description

NM_181484.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.